One goal of regenerative medicine is to be able to convert pluripotent cells into other cell types for tissue repair and regeneration. Human pluripotent cell lines exhibit a level of developmental plasticity that is similar to the early embryo, enabling in vitro differentiation into all three embryonic germ layers (Rossant, 2008; Thomson et al., 1998). At the same time it is possible to maintain these pluripotent cell lines for many passages in the undifferentiated state (Adewumi et al., 2007). These unique characteristics render human embryonic stem (ES) and human induced pluripotent stem (iPS) cells a promising tool for biomedical research (Colman and Dreesen, 2009). ES cell lines have already been established as a model system for dissecting the cellular basis of monogenic human diseases.
However, several recent developments have greatly increased the need for an assay that can predict the behavior of pluripotent human cell lines. First, the continued derivation of human ES cell lines by many labs and the lifting of funding restrictions in the U.S. have substantially increased the number of ES cell lines from which investigators can choose. Additionally, it has become clear that not all human ES cell lines  are equally suited for every purpose (Osafune et al., 2008). This suggests that any new research project should include a deliberate and informed selection of the cell lines that are most qualified for an application of interest.
The ability to reprogram somatic cells from patients into iPS cells has also led to a further increase in the number of pluripotent cell lines available to, and used by, the research community. As investigators gather together existing cell lines, or derive new ones for their application of interest, there is little information or guidance concerning how to select cell lines that are most appropriate for use.
Future applications of human pluripotent stem cell lines will likely include the study of common diseases that arise as the result of complex interactions between a person's genotype and their environment (Colman and Dreesen, 2009). In addition, pluripotent cells will eventually serve as a renewable source of both cells and tissue for transplantation medicine (Daley, 2010). Both of these proposed applications for pluripotent stem cells will require the selection of cell lines that reliably, reproducibly, efficiently and stably differentiate into disease-relevant cell types. However, a significant amount of variation has been reported in the efficiency by which different human ES cell lines or iPSC lines differentiate into different derivatives of the three embryonic germ layers (Di Giorgio et al., 2008; Osafune et al., 2008). Furthermore, it has been reported that iPS cells collectively deviate from ES cells in the expression of hundreds of genes (Chin et al., 2009), and their ability to differentiate down particular lineages (Hu et al., 2010). While some iPS cell lines can differentiate as efficiently as ES cells (Boland et al., 2009; Miura et al., 2009; Zhao et al., 2009), the published gene expression signatures of iPS cells are not reproducible (Stadtfeld et al., 2010). The long-term proliferation and differentiation potential of human pluripotent stem cells suggests that they can produce large quantities of various cell types for disease modeling and transplantation therapy. However, before embryonic stem (ES) cells or induced pluripotent stem (iPS) cells can be used with confidence in therapeutic application or disease modeling, or in drug screening or toxicity assays, the extent of variation between human pluripotent cell lines must be understood. In particular, it is necessary to establish a reference of normal variation among high-quality pluripotent cell lines, in order to provide a baseline against which variation from cell-line to cell-line can be identified and to permit systematic selection of a particular pluripotent stem cell best suited for a particular use.
Therefore, there is a need in the art for novel, effective and efficient methods for characterizing and validating cells, including pluripotent stem cell monitoring and validation, and for determining the quality of the, for example, pluripotent stem cell as well as its propensity to, for example, differentiate along a particular cell lineage, prior to its use, e.g., in therapeutic administration, disease modeling, drug development and screening and toxicity assays etc., to reduce administration of aberrant cells (e.g., non-pluripotent stem cells, or cells that are unlikely to differentiate along a desired lineage).